JavaCommandLineFunctions can now specify the classpath+mainclass as an alternative to specifying a path to an executable jar.
JCLF by default pass on the current classpath and only require the mainclass be specified by the developer extending the JCLF, relieving the QScript author from having to explicitly specify the jar.
Like the Picard MergeSamFiles, GATK engine by default is now run from the current classpath. The GATK can still be overridden via .jarFile or .javaClasspath.
Walkers from the GATK package are now also embedded into the Queue package.
Updated AnalyzeCovariates to make it easier to guess the main class, AnalyzeCovariates instead of AnalyzeCovariatesCLP.
Removed the GATK jar argument from the example QScripts.
Removed one of the most FAQ when getting started with Scala/Queue, the use of Option[_] in QScripts:
1) Fixed mistaken assumption with java enums. In java enums can be null so they don't need nullable wrappers.
2) Added syntactic sugar for Nullable primitives to the QScript trait. Any variable defined as Option[Int] can just be assigned an Int value or None, ex: myFunc.memoryLimit = 3
Removed other unused code.
Re-fixed dry run function ordering.
Re-ordered the QCommandline companion object so that IntelliJ doesn't complain about missing main methods.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5504 348d0f76-0448-11de-a6fe-93d51630548a
- RefMetaDataTracker: grabbing variant contexts given a prefix (not sure where else this was implemented, if someone can show me I'll remove it)
- VCFUtils: grabbing VCF headers given a prefix
- MathUtils: Useful functions for calculating statistics on collections of Numbers
- VariantAnnotator: Made isUniqueHeaderLine a public static method -- maybe this should go into a different class. Not sure.
- Associations: PluginManager now used to propagate classes, implementations for Z,T,U tests, slight alteration to format to make the objects stored
in the window optionally different from those returned by whatever statistic is run across the window
Added:
- MannWhitneyU. Started to fix up WilcoxonRankSum but there are comments in there questioning the validity of some of the code, and I'm sure that
it's actually doing a U test. This implementation includes the direct calculation of p-values for small sample sizes, and a uniform approximation
for when one of the sample sets is small, and the other large. Unit tests to follow.
- BootstrapCallsMerger: takes n VCFs which have been called on the same samples; merges them together while averaging the annotations
- BootstrapCalls.q: qscript for testing the effectiveness of boostrap low-pass calling on the exome
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5372 348d0f76-0448-11de-a6fe-93d51630548a
kshakir
chartl